Prof. Konstantinos Krampis Office: Rm. 467F Belfer Research Building Phone: (212) Fax: (212)

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1 Director: Prof. Konstantinos Krampis Office: Rm. 467F Belfer Research Building Phone: (212) Fax: (212) Facility Consultant:Carlos Lijeron 1/8

2 Office: Rm. 400 Belfer Research Building Phone: (212) Bioinformatician:Baekdoo Kim Office: Rm. 400 Belfer Research Building 2/8

3 Bioinformatician:Thahmina Ali Office: Rm. 400 Belfer Research Building Network Advisor Main Campus Dr. Lloyd Williams Description of the Facility Background Overview The Hunter College/CTBR Bioinformatics resources is located on the 4th floor of the Belfer 3/8

4 Research Building at 69th Street and York Ave. The facility affords access to researchers and faculty, a high-performance computer cluster with a large range of bioinformatics software and data analysis pipelines. The facility provides cutting-edge bioinformatics technology for translational and basic research on health disparities. We also host a web-accessible bioinformatics platform based on Galaxy, ( to support genomic sequencing analysis. Additionally, the facility offers Illumina Sequencing using the Illumina MiSeq sequencing platform and Nanopore sequencing using Oxford Nanopore MinIon sequencer. Both these instruments are capable of sequencing entire complement of DNA, or genome, of many animal, plant, and microbial species for basic biological and medical research. A detailed description of our services and available equipment is given below Services - RNAseq and variation discovery small RNAs sequencing de novo bacterial genomes RNAseq Analysis Targeted amplicon sequencing Computational Capacity Scalable Storage Bioinformatics and Sequencing Resources and Equipment 4/8

5 Illumina MiSeq MiSeq desktop sequencer: Allows narrowly focused applications such as targeted gene sequencing, metagenetics, metagenomics, Oxford Nanopore MinIon sequencer Nanopore(real-time sequencing): MinIon portable sequencer: provides a rapid and portable, real-time sequencing platform that includes s Agilent Technologies, 2100 Electrophoresis Bioanalyzer The Agilent 2100 Bioanalyzer is a microfluidics-based platform that provides sizing, quantitation and qua Two assay principles - electrophoresis and flow cytometry Galaxy Web-accessible Bioinformatics Platform 5/8

6 We are running an instalation of Galaxy. a web based platform for data intensive BioMedical research Silicon Mechanics, HPC Cluster System The high performance computing cluster provides 800 CPU cores, 3TB of high-speed RAM, a GPU Nod - Redundant Head Node, 12 CPU Cores, 64 GB RAM 10 Compute Nodes, 20 CPU Cores each, 128 GB RAM 1 Medium Memory Node, 32 CPU Cores, 512 MB RAM 1 High Memory Node, 32 CPU Cores, 1 Terabyte RAM 1 GPU Node, K80, 2 CPU Hyper-Threaded / 128 GB RA 6/8

7 Seagate Lustre CS1500 ClusterStor 1500 solutions feature scale-out storage building blocks, the Lustre parallel filesystem and - 362TB of parallel storage - 5GB/s throughput - Seagate Enterprise Lustre - Parallel based storage Belfer E-Box The Belfer E-box provides storage for data backup and project archiving TB of high availability storage - 5GB/s throughput Procedure For Submitting Jobs to the Cluster SLURM, Work Load Manager Jobs must be submitted to the cluster using Using SLURM, our job management platform. Vitual environments can be loaded using Conda our package manager. Once you activate your environment and you are sure your application is available, you can simply request srun or sbatch. Follow these steps to use SLURM Get a compute node assigned to you: [username@ctbr-cluster-hn1 env ]$ salloc salloc: Granted job allocation 48 7/8

8 Salloc requests resources form the cluster. The number 48 in the example above is the allocation n er provided to you. You can submit jobs directly to your allocation or run a batch script. Submitting a job using the command SRUN that will make use of the resources allocated. For this example we will use Bowtie2. srun bowtie2 -x Bowtie_2/hg38-1 RNAseq_sample_dat6a/adrenal_1.fastq -2 RNAseq_sample_da srun = Directs the job to the compute node assigned by salloc. bowtie2 = Main binary inside the virtual environment recently activated. Bowtie_2/hg38 = This is the reference human genome RNAseq_sample_data/adrenal_1.fastq = First input strand RNAseq_sample_data/adrenal_2.fastq = Second input strand alignment.sam = The output file will be placed in the current directory A guide on using conda and SLURM can be obtained by clicking here The Bioinformatics and Sequencing Resources is supported by a Research Centers in Minority Institutions Program grant from the National Institute on Minority Health and Health Disparities (MD007599) of the National Institutes of Health. Joomla SEO powered by JoomSEF 8/8